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Yorodumi- PDB-7kx5: Crystal structure of the SARS-CoV-2 (COVID-19) main protease in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kx5 | |||||||||
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Title | Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with noncovalent inhibitor Jun8-76-3A | |||||||||
Components | 3C-like proteinase | |||||||||
Keywords | VIRAL PROTEIN / Mpro / 76-3A / noncovalent / inhibitor / non-covalent / main protease / 3cl / SARS / SARS-CoV-2 / COVID / COVID-19 / 3c-like | |||||||||
Function / homology | Function and homology information protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / TRAF3-dependent IRF activation pathway / snRNP Assembly / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / : / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / copper ion binding / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Sacco, M. / Wang, J. / Chen, Y. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2021 Title: Discovery of Di- and Trihaloacetamides as Covalent SARS-CoV-2 Main Protease Inhibitors with High Target Specificity. Authors: Ma, C. / Xia, Z. / Sacco, M.D. / Hu, Y. / Townsend, J.A. / Meng, X. / Choza, J. / Tan, H. / Jang, J. / Gongora, M.V. / Zhang, X. / Zhang, F. / Xiang, Y. / Marty, M.T. / Chen, Y. / Wang, J. #1: Journal: J.Med.Chem. / Year: 2022 Title: Expedited Approach toward the Rational Design of Noncovalent SARS-CoV-2 Main Protease Inhibitors. Authors: Kitamura, N. / Sacco, M.D. / Ma, C. / Hu, Y. / Townsend, J.A. / Meng, X. / Zhang, F. / Zhang, X. / Ba, M. / Szeto, T. / Kukuljac, A. / Marty, M.T. / Schultz, D. / Cherry, S. / Xiang, Y. / Chen, Y. / Wang, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kx5.cif.gz | 76.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kx5.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 7kx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/7kx5 ftp://data.pdbj.org/pub/pdb/validation_reports/kx/7kx5 | HTTPS FTP |
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-Related structure data
Related structure data | 7rn0C 7rn1C 6yz6 S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33825.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P0DTD1, SARS coronavirus main proteinase | ||||
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#2: Chemical | ChemComp-X7V / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3000, 0.2 M NaF |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.57→50 Å / Num. obs: 7463 / % possible obs: 97.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.069 / Rrim(I) all: 0.13 / Χ2: 1.07 / Net I/σ(I): 6.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6YZ6 6yz6 Resolution: 2.6→38.27 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.857 / SU B: 16.474 / SU ML: 0.349 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.455 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.16 Å2 / Biso mean: 54.243 Å2 / Biso min: 35.68 Å2
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Refinement step | Cycle: final / Resolution: 2.6→38.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.572→2.639 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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